dc.contributor.advisor | de Haan, Hendrick | |
dc.contributor.advisor | Waller, Ed | |
dc.contributor.author | Magill, Martin | |
dc.date.accessioned | 2017-05-02T14:44:33Z | |
dc.date.accessioned | 2022-03-29T17:34:00Z | |
dc.date.available | 2017-05-02T14:44:33Z | |
dc.date.available | 2022-03-29T17:34:00Z | |
dc.date.issued | 2016-12-01 | |
dc.identifier.uri | https://hdl.handle.net/10155/751 | |
dc.description.abstract | A novel nanopore geometry is proposed, in which a larger internal cavity is
located inside a traditional nanopore. Polymer translocation through this geometry
is studied using coarse-grained Langevin dynamics. The most striking
result is that translocation time through the system is found to be minimal
for polymers of medium length: both longer and shorter chains take longer
to translocate. The length at which this occurs is named the critical length.
This phenomenon arises as a balance between the driving electric force field
and the entropic barrier that must be overcome in order for the polymer to exit
the internal cavity. More detailed characterization of the system over a range
of simulation parameters elucidate the physical mechanisms important to this
mechanism. Using these results, a simplified free energy model is constructed
and is solved analytically to predict the critical chain length as a function of
applied field strength and cavity size. Good agreement is recovered between
this theoretical model and numerical measurements over a range of parameters,
and bounds of applicability are discussed. Applications of this new nanopore
design are discussed. | en |
dc.description.sponsorship | University of Ontario Institute of Technology | en |
dc.language.iso | en | en |
dc.subject | Nanopores | en |
dc.subject | Langevin dynamics | en |
dc.subject | Computational | en |
dc.subject | Nanobiophysics | en |
dc.title | Characterization of nanopores with internal cavities for DNA manipulation using Langevin dynamics simulations | en |
dc.type | Thesis | en |
dc.degree.level | Master of Science (MSc) | en |
dc.degree.discipline | Modelling and Computational Science | en |